Houston scientists develop breakthrough AI-driven process to design, decode genetic circuits

biotech breakthrough

Rice University scientists Kshitij Rai, Caleb Bashor and Ronan O’Connell have developed CLASSIC, a new AI-driven process that can generate and test millions of DNA designs at the same. Photo by Jeff Fitlow. Courtesy Rice University.

Researchers at Rice University have developed an innovative process that uses artificial intelligence to better understand complex genetic circuits.

A study, published in the journal Nature, shows how the new technique, known as “Combining Long- and Short-range Sequencing to Investigate Genetic Complexity,” or CLASSIC, can generate and test millions of DNA designs at the same time, which, according to Rice.

The work was led by Rice’s Caleb Bashor, deputy director for the Rice Synthetic Biology Institute and member of the Ken Kennedy Institute. Bashor has been working with Kshitij Rai and Ronan O’Connell, co-first authors on the study, on the CLASSIC for over four years, according to a news release.

“Our work is the first demonstration that you can use AI for designing these circuits,” Bashor said in the release.

Genetic circuits program cells to perform specific functions. Finding the circuit that matches a desired function or performance "can be like looking for a needle in a haystack," Bashor explained. This work looked to find a solution to this long-standing challenge in synthetic biology.

First, the team developed a library of proof-of-concept genetic circuits. It then pooled the circuits and inserted them into human cells. Next, they used long-read and short-read DNA sequencing to create "a master map" that linked each circuit to how it performed.

The data was then used to train AI and machine learning models to analyze circuits and make accurate predictions for how untested circuits might perform.

“We end up with measurements for a lot of the possible designs but not all of them, and that is where building the (machine learning) model comes in,” O’Connell explained in the release. “We use the data to train a model that can understand this landscape and predict things we were not able to generate data on.”

Ultimately, the researchers believe the circuit characterization and AI-driven understanding can speed up synthetic biology, lead to faster development of biotechnology and potentially support more cell-based therapy breakthroughs by shedding new light on how gene circuits behave, according to Rice.

“We think AI/ML-driven design is the future of synthetic biology,” Bashor added in the release. “As we collect more data using CLASSIC, we can train more complex models to make predictions for how to design even more sophisticated and useful cellular biotechnology.”

The team at Rice also worked with Pankaj Mehta’s group in the department of physics at Boston University and Todd Treangen’s group in Rice’s computer science department. Research was supported by the National Institutes of Health, Office of Naval Research, the Robert J. Kleberg Jr. and Helen C. Kleberg Foundation, the American Heart Association, National Library of Medicine, the National Science Foundation, Rice’s Ken Kennedy Institute and the Rice Institute of Synthetic Biology.

James Collins, a biomedical engineer at MIT who helped establish synthetic biology as a field, added that CLASSIC is a new, defining milestone.

“Twenty-five years ago, those early circuits showed that we could program living cells, but they were built one at a time, each requiring months of tuning,” said Collins, who was one of the inventors of the toggle switch. “Bashor and colleagues have now delivered a transformative leap: CLASSIC brings high-throughput engineering to gene circuit design, allowing exploration of combinatorial spaces that were previously out of reach. Their platform doesn’t just accelerate the design-build-test-learn cycle; it redefines its scale, marking a new era of data-driven synthetic biology.”

From Your Site Articles
Ad Placement 300x100
Ad Placement 300x600

CultureMap Emails are Awesome

Property Showcase

Houston medtech startup clears FDA approval for new surgical tool

precision surgery

Houston-based Prana Surgical will soon bring a new electrosurgical tool to operating rooms around the country. The Prana System officially cleared U.S. Food and Drug Administration (FDA) approval earlier this month.

"Receiving FDA clearance for the Prana System represents a defining milestone for our company," Joanna Nathan, CEO and co-founder of Prana Surgical, said in a news release. "Surgeons today are increasingly focused on achieving precise outcomes while minimizing disruption to healthy tissue. The Prana System was designed to support that shift by integrating targeting and excision into a single, streamlined tool."

Prana Surgical began as Prana Thoracic in 2022. Back then, the company primarily focused on developing screening tools for lung cancer diagnosis. It raised $6 million in series A funding rounds in 2023 and 2024 before transitioning to broader surgical needs in 2025.

The Prana System is a minimally invasive, image-guided, single-use tissue extraction tool designed to retrieve samples without damaging healthy tissue. The tool is still designed with the respiratory system in mind, helping Prana in the fight against lung cancer and other thoracic diseases.

Reducing the impact of tissue extraction via electrosurgery and enhanced image scanning can significantly reduce complications. The Prana System combines localization and tissue-cutting capabilities in one, which keeps surgeons from having to swap out components during a procedure, making for a smoother process. It can core, cut and feel blood vessels on the way toward the intended target, giving surgeons greater control over tissue preservation.

"Electrosurgery is foundational to modern surgery, but there is still opportunity to improve how energy-based tools are applied in minimally invasive settings," Nathan added. "Our goal is to introduce a new class of image-guided surgical tools that enable more precise intervention across a range of procedures."

The company projects sales of $7.5 billion from the Prana System in the United States, estimating that 2.5 million surgical modules will be able to use the new tool. While starting out focused on biopsies, the company plans to evolve the system into other procedures, such as ablation, in the future. It is also planning for a controlled U.S. clinical rollout as it moves toward commercialization

Texas still ranks as No. 1 in U.S. for inbound moves, but growth dips

by the numbers

Texas continues to be the country’s No. 1 magnet for newcomers from other states, giving a boost to the state’s economy. However, Texas’ appeal weakened in 2024 compared with the previous year, due in large part to spiking home prices.

An analysis of U.S. Census Bureau data by self-storage platform StorageCafe shows Texas saw net interstate migration of 76,000 people in 2024. Texas’ net interstate migration dropped nearly 50 percent from 2023, according to the analysis. Net migration refers to the number of incoming residents minus the number of outgoing residents.

California remained the top source of newcomers for Texas, sending nearly 77,000 residents to the Lone Star State in 2024, the analysis says. Florida ranked second, followed by New York, Colorado and Illinois.

“These trends reveal Texas’ continued pull from both high-cost coastal markets and other large Sun Belt states, resulting in a mix of affordability-driven and job-driven relocation,” StorageCafe says.

Putting a damper on the influx of new residents: a roughly 124 percent surge in Texas home prices over the past decade, according to StorageCafe.

“While the state remains significantly more affordable than California, its top feeder state, the once-wide pricing gap has narrowed,” says StorageCafe. “For many movers, Texas is still a relative bargain, but no longer an undisputed one.”

Nonetheless, Texas keeps attracting young, highly educated people, which bodes well for the state’s long-term economic outlook, StorageCafe says. More than half of new arrivals to Texas in 2024 held at least a bachelor’s degree, and the age of newcomers averaged 32.

Where are most of these young, highly educated newcomers settling?

Lloyd Potter, former Texas state demographer, tells StorageCafe that population growth in Texas is happening most rapidly in suburban “ring counties” at the expense of slowing growth in urban cores. Ring counties are on the outskirts of major metro areas.

“Many people are moving from urban cores to suburban rings seeking lower costs, newer housing, better schools, and more space,” Potter says. “Typically, a move to a suburban county will be within commuting or hybrid‑commuting distance of major metro economies.”

Artemis II makes historic call to space station with help from Houston Mission Control

History in the making

Still aglow from their triumphant lunar flyby, the Artemis II astronauts made more history Tuesday, April 7: calling their friends aboard the International Space Station hundreds of thousands of miles away as they headed home from the moon.

It was the first moonship-to-spaceship radio linkup ever. NASA's Apollo crews had no off-the-planet company back in the 1960s and 1970s, the last time humanity set sail for deep space.

"We have been waiting for this like you can’t imagine,” Artemis II commander Reid Wiseman called out.

For Christina Koch on Artemis II and Jessica Meir aboard the space station, it marked a joyous space reunion despite being 230,000 miles (370,000 kilometers) apart. The two teamed up for the world's first all-female spacewalk in 2019 outside the orbiting lab.

Koch told her “astro-sister” that she'd hoped to meet up with her again in space “but I never thought it would be like this — it's amazing.”

“I'm so happy that we are back in space together,” Meir replied, “even if we are a few miles apart.”

Houston's Mission Control arranged the cosmic chitchat between the four lunar travelers and the space station's three NASA and one French residents.

Koch described being awe-struck by not just the beauty of Earth, “but how much blackness there was around it.”

“It just made it even more special. It truly emphasized how alike we are, how the same thing keeps every single person on planet Earth alive,” she told the space station crew. “The specialness and preciousness of that really is emphasized” when viewing the home planet from the moon.

By late Tuesday afternoon, the Artemis II astronauts had beamed back more than 50 gigabytes' worth of pictures and other data from the previous day's lunar rendezvous, which set a new distance record for humanity. The highlight: an Earthset photo reminiscent of Apollo 8's Earthrise shot from 1968.

"While they are inspirational and, I think, allow all of us to really feel a little bit of what they were feeling, there's also a lot of science hidden inside of those images," said Mission Control's lead lunar scientist Kelsey Young. “The conversations and the science lessons learned are just beginning."

During a debriefing with Young, the astronauts recounted how they spotted a cascade of pinpricks of light on the lunar surface from impacting cosmic debris. The flashes lasted mere milliseconds and coincided by chance with Monday evening's total solar eclipse.

Young said it was too soon to know whether the crew witnessed an actual meteor shower or more random, run-of-the-mill micrometeoroid hits. Either way, there were “audible screams of delight” in the science operations center, she said.

Koch described being awe-struck by not just the beauty of Earth, “but how much blackness there was around it.”

“It just made it even more special. It truly emphasized how alike we are, how the same thing keeps every single person on planet Earth alive,” she told the space station crew. “The specialness and preciousness of that really is emphasized” when viewing the home planet from the moon.

The first lunar explorers since Apollo 17 in 1972, Wiseman and his crew are aiming for a splashdown off the San Diego coast on Friday to wrap up the nearly 10-day test flight. The recovery ship USS John P. Murtha left port Tuesday for the target zone.

It sets the stage for next year's Artemis III, a lunar lander docking demo in orbit around Earth. Artemis IV will follow in 2028 with two astronauts attempting to land near the lunar south pole.

As for the Orion capsule’s pesky potty, Mission Control assured the astronauts that no maintenance was required Tuesday. The toilet has been on-and-off limits to the crew ever since last week’s launch, prompting them to rely on a backup bag-and-funnel system for urinating.

NASA Administrator Jared Isaacman told the crew following the lunar flyby Monday night: “We definitely have to fix some of the plumbing” ahead of the next Artemis mission. Engineers suspect a clogged filter in the overboard flushing system.

Aside from the toilet and other relatively minor matters, the mission has gone well, Isaacman noted at a news conference Tuesday, “but I'll breathe easier when we get through reentry and everybody's under chutes and in the water.”

View All Listings